Contacts of the strand formed by residues 1473 - 1480 (chain B) in PDB entry 1XTB


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR1473 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1053B  ASP      4.4     1.7    -      -       -      +
   1056B  LYS*     3.0    35.4    +      -       -      +
   1057B  ASN*     3.5    14.0    +      -       -      -
   1403B  CYS*     3.3    13.5    -      -       +      +
   1405B  PHE*     3.9    12.3    -      -       +      -
   1432B  THR*     3.4    28.9    +      -       +      +
   1435B  LEU*     3.4    35.0    -      -       +      -
   1471B  ARG      3.9     5.3    +      -       -      +
   1472B  PRO*     1.3    82.3    -      -       -      +
   1474B  ASN*     1.3    62.5    +      -       -      +
   1475B  SER*     4.9     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN1474 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1052B  LEU*     4.6     8.3    -      -       +      -
   1053B  ASP      3.6     4.0    -      -       -      +
   1054B  TYR*     3.1    15.8    -      -       -      +
   1057B  ASN*     2.8    30.4    +      -       -      +
   1319B  LEU*     3.8    22.8    +      -       -      +
   1322B  LEU*     3.8    11.6    -      -       -      +
   1326B  TYR*     6.2     0.6    -      -       -      -
   1403B  CYS      2.8     5.7    +      -       -      +
   1404B  ASP*     2.9    29.7    +      -       -      +
   1405B  PHE*     2.8    31.0    +      -       -      +
   1473B  THR*     1.3    73.9    -      -       -      +
   1475B  SER*     1.3    61.5    +      -       -      +
   1476B  ILE*     4.0     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER1475 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    544A  LEU*     3.7    36.1    -      -       -      +
   1051B  LEU      3.3     3.5    -      -       -      +
   1052B  LEU*     3.8     0.5    -      -       -      -
   1053B  ASP*     2.9    37.7    +      -       -      +
   1056B  LYS*     4.3     2.6    +      -       -      -
   1405B  PHE      3.4     4.3    -      -       -      -
   1428B  PHE*     4.0    13.7    -      -       -      -
   1432B  THR*     3.7    25.6    +      -       -      +
   1473B  THR*     4.3     0.9    +      -       -      -
   1474B  ASN*     1.3    72.5    -      -       -      +
   1476B  ILE*     1.3    61.6    +      -       -      +
   1477B  VAL*     3.9     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1476 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1050B  ILE*     4.1    23.1    -      -       +      -
   1051B  LEU      3.3     4.5    -      -       -      +
   1052B  LEU*     3.7    23.8    -      -       +      -
   1319B  LEU*     4.6     4.5    -      -       +      -
   1404B  ASP*     4.3     9.4    -      -       -      +
   1405B  PHE      2.7    13.8    +      -       -      +
   1406B  LEU*     3.2    17.8    -      -       +      +
   1407B  ILE      3.1    24.3    +      -       -      +
   1428B  PHE*     4.4     0.2    -      -       -      -
   1474B  ASN*     4.8     2.7    -      -       +      +
   1475B  SER*     1.3    76.8    -      -       -      +
   1477B  VAL*     1.3    61.0    +      -       -      +
   1478B  PHE*     4.0     3.9    -      -       +      -
   1489B  LEU*     4.3    17.3    -      -       +      -
   1492B  MET*     3.8    20.6    -      -       +      -
   1493B  TYR*     3.2    26.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1477 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    544A  LEU*     3.8    25.1    -      -       +      -
    547A  PHE*     3.5    21.2    -      -       +      -
    548A  ILE*     4.4    10.5    -      -       +      -
   1050B  ILE*     3.4     1.7    -      -       -      -
   1051B  LEU*     2.6    40.7    +      -       +      +
   1407B  ILE*     3.4    15.0    -      -       +      +
   1409B  VAL*     3.6    27.1    -      -       +      +
   1428B  PHE*     3.8    28.0    -      -       +      -
   1476B  ILE*     1.3    77.7    -      -       -      +
   1478B  PHE*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1478 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547A  PHE*     4.6     0.9    -      -       -      -
   1049B  HIS      3.1    10.5    -      -       -      +
   1050B  ILE*     4.0    15.5    -      -       +      -
   1344B  LEU*     4.6    10.8    -      -       +      -
   1406B  LEU*     4.2     9.6    -      -       +      -
   1407B  ILE*     3.2    21.1    +      -       -      -
   1408B  PRO*     3.0    43.2    -      -       +      +
   1409B  VAL*     2.7    34.7    +      -       -      -
   1476B  ILE*     4.0     8.3    -      -       +      -
   1477B  VAL*     1.3    78.3    -      -       -      +
   1479B  THR*     1.3    58.8    +      -       -      +
   1480B  LYS      3.7    13.9    -      -       -      -
   1481B  LEU*     3.7    24.2    -      -       +      -
   1485B  ILE*     3.9    13.2    -      -       +      -
   1489B  LEU*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR1479 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547A  PHE*     4.9     1.2    -      -       -      -
    551A  GLN*     2.6    37.2    +      -       -      +
    554A  ALA*     4.3     4.9    -      -       +      -
    556A  ILE*     3.8    21.5    -      -       +      -
   1048B  GLY*     3.8     8.5    -      -       -      -
   1049B  HIS*     2.9    28.4    +      -       -      +
   1409B  VAL*     3.6     9.1    -      -       -      +
   1410B  GLN*     2.8    49.2    +      -       -      +
   1478B  PHE*     1.3    71.0    -      -       -      +
   1480B  LYS*     1.3    59.9    +      -       -      +
   1485B  ILE*     5.8     0.4    -      -       -      +
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Residues in contact with LYS1480 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556A  ILE*     3.5    20.1    -      -       +      +
   1173B  TYR*     4.4     3.2    +      -       -      -
   1408B  PRO*     4.0     6.7    -      -       -      -
   1410B  GLN*     3.6    33.5    -      -       +      +
   1411B  THR      4.3    14.1    +      -       -      -
   1412B  GLN*     3.4    35.3    +      -       -      +
   1478B  PHE*     3.3     6.8    +      -       -      -
   1479B  THR*     1.3    81.0    -      -       -      +
   1481B  LEU*     1.3    62.8    +      -       -      +
   1482B  THR*     3.1    18.8    +      -       +      +
   1485B  ILE*     3.3    24.5    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il